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open2c
cooler

A cool place to store your Hi-C

17K 237 60
open2c
pairtools

Extract 3D contacts (.pairs) from sequencing alignments

14K 131 37
Siegel-Lab
libbiosmoother

On-the-fly processing and visualization of interactome data.

6K 0 1
koszullab
hicstuff

Simple library/pipeline to generate and handle Hi-C data.

4K 39 8
higlass
clodius

Clodius is a tool for breaking up large data sets into smaller tiles that can subsequently be displayed using an appropriate viewer.

4K 39 22
4dn-dcic
hic2cool

Lightweight converter between hic and cool contact matrices.

4K 74 10
rjdkmr
gcmapexplorer

Genome Contact Map Explorer - gcMapExplorer. Visit:

3K 21 9
4dn-dcic
pypairix

1D/2D indexing and querying on bgzipped text file with a pair of genomic coordinates

2K 92 15
koszullab
chromosight

Computer vision based program for pattern recognition in chromosome (Hi-C) contact maps

2K 71 11
ay-lab
mustache-hic

Multi-scale Detection of Chromatin Loops from Hi-C and Micro-C Maps using Scale-Space Representation

2K 82 13
XiaoTaoWang
tadlib

A Library to Explore Chromatin Interaction Patterns for Topologically Associating Domains

1K 45 12
XiaoTaoWang
hiclift

Convert genomic coordinates of contact pairs from one assembly to another.

1K 78 5
koszullab
metator

Metagenomic binning based on Hi-C data

1K 28 10
open2c
coolpuppy

A versatile tool to perform pile-up analysis on Hi-C data in .cool format.

747 81 13
XiaoTaoWang
neoloop

A computation framework for genome-wide detection of enhancer-hijacking events from chromatin interaction data in re-arranged genomes

730 76 18
XiaoTaoWang
runhic

An easy-to-use Hi-C data processing software supporting distributed computation.

687 62 22
koszullab
instagraal

Large genome reassembly based on Hi-C data, continuation of GRAAL

662 43 10
seqyuan
trackc

trackc aims to produce beautiful genome tracks that are highly customizable

616 18 0
cmdoret
pareidolia

Multi-sample change detection in Hi-C patterns

610 9 3
XiaoTaoWang
hicpeaks

A Python implementation for BH-FDR and HiCCUPS

464 54 11
Tian-Dechao
diffdomain-py3

DiffDomain is a statistically sound method for detecting differential TADs between conditions

405 18 5
Siegel-Lab
biosmoother

On-the-fly processing and visualization of interactome data

405 5 0
vaquerizaslab
chess-hic

Comparison of Hi-C Experiments using Structural Similarity.

386 27 6
cmdoret
hicreppy

Python reimplementation of hicrep with compatibility for sparse matrices

367 19 3
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